# HG changeset patch
# User serranop
# Date 1379106010 14400
# Node ID cb90b8246ef2ff07211cd09023bce33e7588d38b
# Parent  3244a7ca3faa66040d44fa36d0fa711f583e848f
New options

diff -r 3244a7ca3faa -r cb90b8246ef2 usearch_fastq_mergepairs.xml
--- a/usearch_fastq_mergepairs.xml	Fri Sep 13 16:11:26 2013 -0400
+++ b/usearch_fastq_mergepairs.xml	Fri Sep 13 17:00:10 2013 -0400
@@ -6,20 +6,62 @@
 -quiet
 -fastq_mergepairs '$input_forward'
 -reverse '$input_reverse'
-#if $minovlen == "0"
-    -fastq_minovlen 1
-#else
+#if $minovlen.value != 0
     -fastq_minovlen $minovlen
 #end if
+#if $minmergelen.value != 0
+    -fastq_minmergelen $minmergelen
+#end if
+#if $maxmergelen.value != 0
+    -fastq_maxmergelen $maxmergelen
+#end if
+#if $maxdiffs.value != 0
+    -fastq_maxdiffs $maxdiffs
+#end if
+#if $truncqual.value != 0
+    -fastq_truncqual $truncqual
+#end if
+#if $minlen.value != 0
+    -fastq_minlen $minlen
+#end if
+$allowmergestagger
+-fastq_ascii $ascii
+-fastq_qmin $qmin
 -fastq_qmax $qmax
--fastqout '$output'
+-fastq_qmaxout $qmaxout
+#if $output_format.format == "fastq"
+    -fastqout $output
+#else
+    -fastaout $output
+#end if
     </command>
     <inputs>
+        <!-- INPUT OPTIONS -->
         <param name="input_forward" type="data" format="fastq,fastqsanger,fastqcssanger" label="File with forward reads" />
         <param name="input_reverse" type="data" format="fastq,fastqsanger,fastqcssanger" label="File with reverse reads" />
         <param name="minovlen" type="integer" value="0" label="Minimum length of the overlap" help="'0' means no minimum." />
+        <param name="minmergelen" type="integer" value="0" label="Minimum length of the merged read" help="'0' means no minimum." />
+        <param name="maxmergelen" type="integer" value="0" label="Maximum length of the merged read" help="'0' means no maximum." />
+        <param name="maxdiffs" type="integer" value="0" label="Maximum number of mismatches allowed in the overlap region" help="'0' means any number of mismatches allowed" />
+        <param name="truncqual" type="integer" value="0" label="Truncate the forward and reverse reads at the first Q<=q, if present. This truncation is performed before aligning the pair. With Illumina paired reads, it is recommended to use ‑fastq_trunqual 2 or higher, as low-quality tails will otherwise often cause alignment of the pair to fail." help="'0' means no quality truncation." />
+        <param name="minlen" type="integer" value="0" label="Minimum length of the forward and reverse read, after truncating per ‑fastq_truncqual if applicable." help="'0' means no minimum." />
+        <param name="allowmergestagger" type="boolean" truevalue="-fastq_allowmergestagger" falsevalue="" checked="false" label="Allow merge of a pair where the alignment is staggered like this: --FORWARD
+  REVERSE--" help="By default, pairs with staggered alignments are discarded." />
+        <param name="ascii" type="integer" value="33" label="ASCII_BASE constant" help="See http://drive5.com/usearch/manual/fastq_params.html" />
+        <param name="qmin" type="integer" value="0" label="Minimum Q score" />
         <param name="qmax" type="integer" value="41" label="Maximum Q score for input files" />
-    </inputs>
+        <param name="qmaxout" type="integer" value="41" label="Maximum Q score for output files" />
+
+        <!-- OUTPUT OPTIONS -->
+        <conditional name="output_format">
+            <param name="format" type="select" display="radio" label="Output format">
+                <option value="fastq">FASTQ</option>
+                <option value="fasta">FASTA</option>
+            </param>
+            <when value="fastq"></when>
+            <when value="fasta"></when>
+        </conditional>
+   </inputs>
     <outputs>
         <data name='output' format='fastq' label="Merge result" />
     </outputs>
@@ -71,10 +113,6 @@
 
 ------
 
-**Author**
-
-Robert C. Edgar (robert@drive5.com)
-
 **Manual**
 
 http://drive5.com/usearch/manual/fastq_mergepairs.html